Variant report

Variant	rs11689392
Chromosome Location	chr2:73622026-73622027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73606604..73608316-chr2:73620841..73623295,2	K562	blood:

Extended variants
information (count: 141 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10165862	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10169213	0.80[EUR][1000 genomes]
rs10170786	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178678	0.83[EUR][1000 genomes]
rs10179134	0.94[EUR][1000 genomes]
rs10183818	0.87[EUR][1000 genomes]
rs10184268	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186501	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	0.87[EUR][1000 genomes]
rs10187416	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189574	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190219	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10193972	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195357	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195358	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197409	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198549	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs10199224	0.84[EUR][1000 genomes]
rs10207220	0.80[EUR][1000 genomes]
rs10207264	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496191	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496192	0.88[CEU][hapmap]
rs10496193	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052162	1.00[ASN][1000 genomes]
rs11126395	0.81[AMR][1000 genomes]
rs11126396	0.81[AMR][1000 genomes]
rs11126404	1.00[ASN][1000 genomes]
rs1114380	0.80[EUR][1000 genomes]
rs11674602	0.86[EUR][1000 genomes]
rs11676385	0.88[EUR][1000 genomes]
rs11679809	0.92[EUR][1000 genomes]
rs11686019	1.00[ASN][1000 genomes]
rs11689588	0.82[EUR][1000 genomes]
rs11693586	0.86[EUR][1000 genomes]
rs11693588	0.86[EUR][1000 genomes]
rs11884776	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs11898362	0.81[AMR][1000 genomes]
rs11899740	0.94[EUR][1000 genomes]
rs11899902	0.95[EUR][1000 genomes]
rs11901272	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903916	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383871	0.94[EUR][1000 genomes]
rs13384952	0.87[EUR][1000 genomes]
rs13385564	0.84[EUR][1000 genomes]
rs13392691	0.86[EUR][1000 genomes]
rs13392872	0.86[EUR][1000 genomes]
rs13398956	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13400985	0.87[EUR][1000 genomes]
rs13409668	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13411311	0.86[EUR][1000 genomes]
rs13421462	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13428235	0.95[EUR][1000 genomes]
rs1403284	0.88[EUR][1000 genomes]
rs1403412	0.84[AMR][1000 genomes]
rs1522926	0.82[AMR][1000 genomes]
rs1534471	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009149	0.80[EUR][1000 genomes]
rs17009159	0.80[EUR][1000 genomes]
rs1852644	0.84[AMR][1000 genomes]
rs1881245	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918863	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056486	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140195	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421550	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421552	0.84[EUR][1000 genomes]
rs2421555	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421577	1.00[ASN][1000 genomes]
rs2901437	0.84[AMR][1000 genomes]
rs2901438	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738848	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813227	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4500972	0.87[ASN][1000 genomes]
rs56014217	0.95[EUR][1000 genomes]
rs56145559	0.91[EUR][1000 genomes]
rs56154726	0.87[EUR][1000 genomes]
rs56672945	0.96[EUR][1000 genomes]
rs58603761	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60844734	0.96[EUR][1000 genomes]
rs62151646	0.89[EUR][1000 genomes]
rs62151652	0.89[EUR][1000 genomes]
rs6546827	0.88[CEU][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes]
rs6546835	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546836	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546837	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546838	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546839	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546845	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546847	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546849	1.00[ASN][1000 genomes]
rs6546850	1.00[ASN][1000 genomes]
rs6546851	1.00[ASN][1000 genomes]
rs6546852	1.00[ASN][1000 genomes]
rs6546853	1.00[ASN][1000 genomes]
rs6546856	1.00[ASN][1000 genomes]
rs6546858	1.00[ASN][1000 genomes]
rs6704782	0.82[EUR][1000 genomes]
rs6705489	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6706409	0.87[AMR][1000 genomes]
rs6707722	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708766	0.86[EUR][1000 genomes]
rs6711033	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6719753	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724782	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735946	0.80[EUR][1000 genomes]
rs6736866	0.91[EUR][1000 genomes]
rs6740223	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.80[EUR][1000 genomes]
rs6741067	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6745480	1.00[ASN][1000 genomes]
rs6753344	0.91[EUR][1000 genomes]
rs6755217	0.93[EUR][1000 genomes]
rs6755241	0.93[EUR][1000 genomes]
rs6756885	0.94[CEU][hapmap]
rs6756987	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73947808	0.87[EUR][1000 genomes]
rs7564890	0.92[EUR][1000 genomes]
rs7566385	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567585	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	0.87[EUR][1000 genomes]
rs7576245	1.00[ASN][1000 genomes]
rs7580750	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580825	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7583255	0.80[EUR][1000 genomes]
rs7584575	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585004	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585124	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586463	0.80[EUR][1000 genomes]
rs7588169	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7598396	0.91[EUR][1000 genomes]
rs7598419	0.80[EUR][1000 genomes]
rs7598946	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602980	0.87[EUR][1000 genomes]
rs7604682	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607014	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309473	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs9653557	0.80[EUR][1000 genomes]
rs9749859	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9753079	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807961	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11689392	ALMS1P	cis	Artery Tibial	GTEx
rs11689392	ALMS1P	cis	Whole Blood	GTEx
rs11689392	ALMS1	cis	normal skin	skin_eQTL
rs11689392	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73614000-73626200	Weak transcription	Lung	lung
2	chr2:73614200-73626200	Weak transcription	HSMM	muscle
3	chr2:73614400-73626200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:73614400-73626400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:73614400-73626400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:73614600-73641600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:73614800-73625200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:73614800-73628600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:73615000-73626200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr2:73615000-73626200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:73615000-73626400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:73615000-73626400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:73615000-73626600	Weak transcription	Ovary	ovary
14	chr2:73615000-73628400	Weak transcription	Hela-S3	cervix
15	chr2:73615000-73645400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:73615000-73646800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:73615200-73626000	Weak transcription	Primary T cells from cord blood	blood
18	chr2:73615200-73626200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:73615200-73626200	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:73615200-73626200	Weak transcription	Thymus	Thymus
21	chr2:73615200-73646400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:73616000-73626200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:73616200-73625000	Weak transcription	Dnd41	blood
24	chr2:73616400-73626200	Weak transcription	HepG2	liver
25	chr2:73620000-73641200	Weak transcription	Osteobl	bone
26	chr2:73620800-73624800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:73621400-73624200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:73621600-73626600	Weak transcription	Small Intestine	intestine
29	chr2:73621800-73626400	Weak transcription	Fetal Stomach	stomach
30	chr2:73622000-73625000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:73622000-73626200	Weak transcription	Fetal Lung	lung
32	chr2:73622000-73648000	Weak transcription	Fetal Kidney	kidney

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